A field mini-plot experiment was conducted on clay loamy oxisol using 32P trace technique when P fertilizer was applied in three depth soil (15, 35 and 55 cm soil layer) to compare P absorption, distribution and translocation in plant organ and soil profile under soybean and citrus monoculture and intercropping at Taoyuan Experimental Station of Agroecosystem Research of Chinese Academy of Science. Total P uptake (PT) and P accumulation in different parts (PA) of soybean were remarkably decreased under intercropping. When 32P was applied in topsoil (15 cm soil layer), 32P uptake (32PT) by soybean was significantly lower in intercropping than in monoculture. Whereas 32PT uptake by soybean was significantly greater in intercropping than in monoculture when 32P was applied in deep soil layer (35 cm or 55 cm soil layer). However, considerable difference was not observed for 32P translocation and distribution among soybean organs. 32PT uptake by citrus was much lower under intercropping than under monoculture. The P uptake by citrus newly could be transferred rapidly to aboveground and prior to active growing organ. Intercropping did not affect 32P distribution in citrus organ, but when P was applied in deep soil layer, the speed of 32P transferred to aboveground and active organ was slowed down. P mobility was strengthened in soil profile, and P of deep soil layer was promoted to move to topsoil in intercropping. The experimental results showed the optimal depth of applied P should be within 20 cm soil layer in soybean-citrus intercropping system.